On Wed, 25 Oct 2000, Carl Virtanen wrote:
> Hi folks,
>> I'm a little new at checking out some of this stuff, so please bear with me. I'm using bioperl 6.2.
> The problem i'm having is that the output from the Blast->to_html routine is not picking up all of the correct references and 'htmlifying' them (see my example near the bottom). I'm just using the standard kinda usage:
> use Bio::Tools::Blast qw(:obj);
> $Blast->to_html(file=>$ARGV[0]);
>> I've narrowed the problem down to the HTML.pm module. Now, call me a
> bonehead (if you wish, but that wouldn't be really nice now would it?)
> but the regexps in there are some real bad ass ones (if you'll excuse
> my colourful explanation)! So tracking down where the problem is is
> not so easy for me. Actually, if somebody would explain to me at
> least one of the regexps,for example:
>> s@^ ?(gb|emb|dbj)\|($Word)(\|$Word)?($Descrip)($Int +)($Signif)(.*)$@$1:<a hre
> f="$DbUrl{'gb_n'}$2">$2$3</a>$4$5<A href="\#$2_A">$6</a>$7<a name="$2_H"></a>@o;
Apologies. That looks like a _beast_.
This one is for stevec if he is tuning in. I have to admit, I tend to
generate html files myself by going through the loops
foreach $hit ( ... ){
foreach $hsp ( ... ) {
}
}
etc. But that is more coding for you....
>>> then i would be very grateful and would even try to track down the problem myself and possibly contribute a little to all of this. I'm familiar with basic regexps/substitution and so on, but yikes!
>> Anyways, here's the output, and you can see that it's missing a bunch of gi's. The search was just a routine peek at some proteins in the nr database:
>> Sequences producing significant alignments: (bits) Value
>> emb|CAB55683.1| (AL035427) dJ769N13.1 (KIAA0443 protein.) [Homo ... 214 2e-54
> ref|NP_055525.1| KIAA0443 gene product >gi|7512985|pir||T00068 h... 214 2e-54
> dbj|BAB14367.1| (AK023031) unnamed protein product [Homo sapiens] 181 2e-44
> gb:AAF64273.1|AF208859_1 (AF208859) BM-017 [Homo sapiens] >gi|82... 123 6e-27
>>>> Thanks!
>> Carl Virtanen
>>>
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